Hi all,
I've been testing out using Modeller to build ferredoxins (some of the
ones in the examples, actually) containing 4Fe-4S cluster(s). I wanted
to try different levels of description, so to start out I've been
describing the FeS clusters as BLK residues. This works very well for
single-template modeling, but when I try to use e.g. 3 template
structures, I get 3 times as many atoms in the model cluster as I
wanted. I've attached the top and alignment files but there are 3 input
atom files (plus the model), so I'll send those on request (in the input
atom files I use, the residue names have been changed to BLK and some of
the atomnames have been changed from the original pdb, so that they all
describe the same position: using the original pdbs should still give
you the same problem of excess atoms, but the clusters will be distorted).
Does anyone have a reason for this, or a way out (apart from deleting
the 'extra' atoms afterwards)?
I'll be building a new FS4 residue anyway; has anyone done that previously?
Many thanks in advance,
Lucy Forrest
# Modeller input script
# LRF 14mar02
# Build models of 2fdn using 3 template pdbs simultaneously
# and multiple alignment
#
# This script should produce one model, 2fdn.B99990016
# try HETERO atoms
#
SYSTEM COMMAND = 'cp 2fdn_3_template_1.ali~ 2fdn_3_template_1.ali'
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1
SET ALNFILE = '2fdn_3_template_1.ali'# alignment filename
SET KNOWNS = '1DUR' '1BLU' '1CLF' # codes of the templates
SET SEQUENCE = '2fdn' # code of the target
SET HETATM_IO = 'on' # use Fe/S heteroatoms
SET ATOM_FILES_DIRECTORY = '../atom_files.d/' # directories for input pdb
SET STARTING_MODEL= 16 # index of the first model
SET ENDING_MODEL = 16 # index of the last model
SET FINAL_MALIGN3D = '1' # make fitted structures
# thorough MD only
#SET MD_LEVEL = 'refine_4'
# Repeat the whole cycle x times and do not stop unless obj.func. > 1E6
SET REPEAT_OPTIMIZATION = 3, MAX_MOLPDF = 1E6
CALL ROUTINE = 'model' # do homology modelling
>P1;1DUR
structureX:1DUR:1 :A:102 :A:::-1.00:-1.00
AYVINDSCIACGACKPECPVNCIQEG-SIYAIDADSCIDC------GSCASVCPVGA-----PNPED--------
-----/..*
>P1;1BLU
structureX:1BLU:1 : :102 : :::-1.00:-1.00
ALMITDECINCDVCEPECPNGAISQGDETYVIEPSLCTECVGHYETSQCVEVCPVDCIIKDPSHEETEDELRAKY
ERITG/..*
>P1;1CLF
structureN:1CLF:1 : :102 : :::-1.00:-1.00
AYKIADSCVSCGACASECPVNAISQGDSIFVIDADTCIDC------GNCANVCPVGAPVQE--------------
-----/..*
>P1;2fdn
sequence:2fdn:. :.:. : :::-1.00:-1.00
AYVINEACISCGACEPECPVNAISSGDDRYVIDADTCIDC------GACAGVCPVDAPVQA--------------
-----/..*
